Never Going to Leave You
by Louisaxo
Summary: A story set during City of Bones and at the end of the first series of Shadowhunters. When Clary wakes Jocelyn, her awakening isn't happy for long when Jocelyn reveals details of Valentine's plans. Clary and Jace pairing - not siblings
1. Chapter 1

**Never Going to Leave You**

 **Chapter One**

 **I am returning to you guys with something new! I know that the Mortal Instruments series isn't everyone's cup of tea, but I absolutely love it. For me, I didn't love the ending of City of Heavenly Fire, and the show doesn't really do the books justice, even though I love the actors and actresses portraying the characters.**

"Come on, Clary." Jocelyn took a hold of Clary's wrist and began to pull her towards the institute exit.

Clary shot an alarmed look at Jace and Isabelle, who were standing a few feet away. Jocelyn had barely woken from her sleep coma and said hello before she was pulling Clary away.

"Mom, what are you doing?" Clary tugged on her own wrist, trying to free herself from Jocelyn's grasp.

"We're going. Neither of us belong here, Clary. We have to go back to the life we were living before, it's safer."

"Safer?" Jace questioned, stepping away from Izzy and moving towards Clary, "You can't be serious. Surely you know that Valentine is still out there. Do you really think that out there is the safest place for Clary right now?" Jace continued, pointing towards the church door a few metres away.

Jocelyn spun on her heel to face Jace, her face showing that she was clearly agitated.

"I think I know what is best for my daughter, thank you very much."

"Jocelyn, Jace is right. The streets of New York are unsafe right now, especially for a trainee Shadowhunter like Clary." Luke stepped forward, putting his hand on Jocelyn's shoulder.

" _I_ am her mother, and I'll be damned if you think I don't know what is best for her. I have taken care of her for her whole life, keeping her out of this world." Jocelyn argued, still gripping Clary's wrist in her hand.

"Mom, remaining here is what will keep me safe. I have fought so hard to get you back. I've been training with Izzy and Jace, and I have been leaning about this life." Clary tried to reason with her mother, to no avail.

"Clary, you know _nothing_ of this world. You have no idea how truly dangerous this world is. You can never live a normal life, you can never fall in love, or truly be happy. Take it from somebody who had to sacrifice her life to keep you safe." Jocelyn continued to argue, completely missing the shocked look on Clary's face.

" _Sacrifice._ " Clary spat the word as though she had venom in her mouth, she tore her wrist from her mother's grasp, taking a step backwards towards Jace.

"Clary, I…" Jocelyn started, only to be interrupted by her daughter.

"I understand why you tried to keep me out of this world, but surely you didn't think you could keep me out of it altogether? I'm sorry mom, but I can't come with you. I have pledged my allegiance to the institute, and I will help them take down Valentine if it is the last thing I ever do." Tears streamed down Clary's pale face as she turned on her heel and ran from the training room.

"Clary!" Izzy called after her, chasing after her. Everyone in the training room heard the clatter of Izzy's heels fade as she walked further away.

"She'll be okay, I think today has just been too much for her. I'll go after them, but you can't take her away from here Jocelyn, this is where she's safest and you know that." Jace spoke calmly, before exiting the room with Alec to track down Izzy and Clary. They found them in Izzy's bedroom, sitting on the bed.

"She didn't mean it Clare, she's probably just confused about what she just went through." Izabella tried to comfort Clary, her hand on her shoulder.

"It doesn't matter whether she's confused or not, what she said is true. She did sacrifice being a Shadowhunter for me." Clary muttered, the three people in the room could barley hear her.

"But that was her choice Clary, you had no control over your mother's choices." Jace said, moving closer to the upset girl on the bed, Izzy got up and stood next to her brother so that Jace could take her spot on the bed.

"It doesn't change the fact that she's right. What is she's right about me never truly being happy and…" Jace cut her off.

"Clary, pay no mind to what Jocelyn said. You must do exactly what makes _you_ happy, and not anybody else. If you're happy here, and you feel safe here you stay and if you aren't, then you are free to leave with your mother." Jace raised his hand and rested it on Clary's cheek, using his thumb to wipe away her tears.

"Do you want to go?" Jace all but whispered, showing his own feelings and emotions as he spoke. It was clear that the thought of Clary leaving terrified Jace.

Clary smiled, raising her own hand and resting it on the one Jace had placed on her face.

"Of course, I don't want to go."

…

Something had been ebbing at Clary since she had spoken with her mother. Why was her mother being so paranoid about her being unsafe, and why didn't she think Clary was safe in the institute?

Clary knocked on the door to her mother's temporary bedroom timidly, poking her head about the door when her mother told her to enter.

"Mom, can I ask you something?"

Jocelyn simply nodded, standing up from the desk she had been sitting at.

"Why are you so adamant about the institute not being safe? Did you hear something that Valentine said, or do you just want to leave?"

"Valentine would never hurt you Clary, but you still have to be careful with the people you surround yourself with. How well do you really know these people? What do you know about them, really?" Jocelyn eyed the open door warily.

"I do know them. Izzy has become like my best friend, and each day I'm getting to know Alec more and more. They've become like siblings really fast, and they've been so helpful in getting you back from Valentine. But Jace, he's different. He's been there for me since the very beginning, he was the person who noticed that I was a Shadowhunter and saved my life when I was attacked at home." Clary finished, surprised at the confused expression that remained on her mother's face.

"You love him." Jocelyn stated shortly.

Clary's eyebrows rose in surprise at what her mother said. She opened her mouth to deny her mothers claim, but then closed it again.

"You didn't answer my question." Clary crossed her arms and watched her mother take a step towards her.

"Valentine knows the location of the New York Institute, it's only a matter of time before he figures out a way to penetrate the wards." Jocelyn explained.

"But you just said that he wouldn't hurt me."

"He wouldn't, but that doesn't mean that he wouldn't take things from you." Jocelyn continued to explain.

"You mean the Mortal Cup?" Clary rolled her eyes, she was really starting to hate that damned cup.

"Well, yes and…" Jocelyn was interrupted when Alec rushed into the room, a panicked expression on his face.

"Alec what's hap…" Clary stopped speaking when a siren started blaring into the room.

"The institute has been infiltrated." Alec spoke quickly before turning on his heel and leaving the room. Clary turned to her mother, who had a knowing expression on her face, she knew this would happen.

"We have to find Jace and the others." Clary cried before following Alec out of the room.

 _ **A little bit of a cliff-hanger for my first chapter, I hope you enjoyed it!**_

 _ **As always, lots of love,**_

 _ **Louisaxo**_


	2. Chapter 2

**Never Going to Leave You**

 **Chapter Two**

 **I am returning to you guys with something new! I know that the Mortal Instruments series isn't everyone's cup of tea, but I absolutely love it. For me, I didn't love the ending of City of Heavenly Fire, and even though I love the actors and actresses portraying the characters, I still love the way fiction writers portray the series.**

Clary and Alec ran into the main room of the institute, where Isabelle and Jace were already standing in front of a screen, trying to determine what had infiltrated their wards. The loud alarm continued to sound around the room, and it was making Clary's head pound.

"Alec, turn that off, would you?" Alec nodded once, knowing exactly what Clary meant. He took his phone from his pocket and touched the screen a few times, Clary sighed when the alarm stopped, and she could finally focus.

"What is it?" Clary asked from her position besides Jace.

"We don't know. We know it's not a demon, the wards system would have flagged that as soon as the wards were breached." Jace said, touching the screen in front of them and bringing up an aerial view of the institute.

"So, does that mean it's a Shadowhunter?" she questioned.

"It's a possibility. The institute wards are magic, they know who has and who hasn't entered them before." Izzy explained.

"Let's see who has decided to pay us a visit then." Jace took his _seraph_ blade from where it was placed at his hip and headed for the door, followed closely by Isabelle, Alec and Clary.

"Clary, no! You must stay." Jocelyn commanded as she saw Clary headed towards the door with the others.

"Mom, I'm not going to leave them to deal with this alone. If this is Valentine, this is my fight too." Jocelyn opened her mouth to argue but Clary was already out of the door.

The four young Shadowhunters stood on the steps of the institute, each of them grateful that they were already in fighting gear before the wards were breached.

"The wards don't go past the treeline, they have to be out here." Alec's eyes narrowed as he looked towards the treeline, trying to see any threat that may be lurking behind it.

"Right you are, my boy. You Lightwood's were always applauded for your knowhow."

Each of them took a few steps forward when the threat stepped into sight. Clary was right, it _was_ a Shadowhunter.

"What do you want, _Valentine,_ if you're here to take my mother you may as well leave now." Clary sneered the man's name.

"Now, now, my daughter. I am not here for Jocelyn, I am here for you my dear child." Clary's eyebrows rose in surprise.

"Well, you're out of look there too. Clary isn't going anywhere with you either." Jace spoke confidently, Clary took an instinctive step closer to him.

It was then that Clary remembered what her mother had said, or _hadn't_ said, when they were talking earlier. Jocelyn had said that Valentine would try to take something from her.

"You want something from me, what is it?" Clary called out to her father, who smirked and took a step towards the four Shadowhunters.

"You're special, Clary. Unlike any other Shadowhunter who has ever existed. I'm sure that when I tell you why, things will start to add up for you. Even though you have only been a Shadowhunter for a matter of weeks, you have managed to pick it up surprisingly, fast haven't you? Your fighting ability is better than those who have been Shadowhunters for their whole lives. You have been able to pick up the ancient art of runes remarkably fast, but given your _abilities_ you have been seeing runes for years, isn't that right?" Valentine smirked knowingly, instantly Clary's sketchbook came to mind, she _had_ been drawing runes, long before she had even known of the Shadow World.

"What do you mean, _abilities?"_ Clary picked up on Valentine's use of the word.

"Like I said, your special clary. Its all about the blood." Valentine laughed once more before turning on his heel and walking into a portal that appeared behind him.

"That was odd, right? Why say he's here for me and then just leave?" Clary questioned.

…

Only minutes had passed since the confrontation, but Clary and Izzy were already in the weapons room putting their weapons and armour back. Alec and Jace had remained outside, checking the perimeter to ensure the institute was safe and secure.

One word continued to run through Clary's mind as she changed back into her normal clothes. She put her blouse back on before stepping out of the changing room that was inside of the weapons room. Immediately Izzy noticed that Clary was lost in thought.

"What's on your mind?"

"Something Valentine said, what did he mean by blood? I already know he's my father, so what is he talking about?" Clary spoke quietly in case somebody else were to walk into the room unannounced.

"I don't know, Clare. I could always sample it, if that is something that you wanted to do." She offered.

"Maybe I'm just being paranoid." Clary brushed it off.

"Better to be safe than sorry." Alec said as he walked further into the room. Clary had been so deep in thought that she hadn't noticed Alec and Jace walk in.

"Do you think?"

"Alec's right. Besides, if it'll make you less worried, its worth a shot." Jace said, coming to Clary's side, she leant into his side instinctively.

…

The four young Shadowhunters stood in an empty lab inside of the institute. Izzy had put a slide with a sample of Clary's blood on below the microscope lens and was studying it intently. Izzy's eyebrows furrowed, causing Clary's eyes to widen in alarm.

"What's wrong?"

"The cells are different. With Shadowhunter blood its distinguishable which cells are angel and which are mundane, but yours consists of more of one type of cell. Look at this one, this is Alec's, compared to yours." Izzy pulled up to photos onto a screen. You could see clearly that Clary's was on the right and Alec's was on the left.

"So why do I have more mundane cells?" Clary asked, slightly worried.

"You don't, Clary, you have more angel cells." Izzy explained, still confused.

"But why? And how?" Clary questioned, alarmed.

"When a Shadowhunter is born, they are half mundane and half angel, this doesn't add up. I'll get Magnus, maybe he can help." Alec touched Izzy's shoulder and together they left the lab, in search of Magnus.

"What is wrong with me?" Clary murmured, although the question was meant to be rhetorical, Jace answered anyway.

"Nothing is wrong with you, Clary. We gat our Shadowhunter abilities from our angel side, so if anything, your abilities will be amplified.

"What will happen if everyone finds out. They'll think I'm a freak."

"Clary, they won't. If anything, having extra abilities is an amazing thing for a Shadowhunter to have in their arsenal.

"What about you?" Clary's eyes rose to meet Jace's, terrified.

"What about me?"

"Will you leave too? I'm sure you don't want to be with someone like me." A tear escaped Clary's eye and ran down her face. Jace raised his hand and wiped it away with his thumb.

"It doesn't matter Clary, you are to me who you always have been. _My Clary._ I'm never going to leave you." He tried to reassure her.

"You promise?"

"I promise." Clary finally smiled and stepped into Jace's embrace, waiting for Izzy and Alec to return with Brooklyn's High Warlock.

Clary knew that with her Shadowhunter family at her side, as well as the person she loved, she would be just fine.

 _ **Thanks for reading guys. Please don't forget to let me know what you thought!**_

 _ **Lots of love,**_

 _ **Louisaxo**_ **  
**


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